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The Nuclear Localization Pattern and Interaction Partners of GTF2IRD1 Demonstrate a Role in Chromatin Regulation

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The Nuclear Localization Pattern and Interaction Partners of GTF2IRD1 Demonstrate a Role in Chromatin Regulation Hum Genet DOI 10.1007/s00439-015-1591-0 ORIGINAL INVESTIGATION The nuclear localization pattern and interaction partners of GTF2IRD1 demonstrate a role in chromatin regulation Paulina Carmona‑Mora1 · Jocelyn Widagdo2 · Florence Tomasetig1 · Cesar P. Canales1 · Yeojoon Cha1 · Wei Lee1 · Abdullah Alshawaf3 · Mirella Dottori3 · Renee M. Whan4 · Edna C. Hardeman1 · Stephen J. Palmer1 Received: 11 February 2015 / Accepted: 4 August 2015 © Springer-Verlag Berlin Heidelberg 2015 Abstract GTF2IRD1 is one of the three members of the mostly involved in chromatin modification and transcrip- GTF2I gene family, clustered on chromosome 7 within a tional regulation, whilst others indicate an unexpected role 1.8 Mb region that is prone to duplications and deletions in connection with the primary cilium. Mapping of the sites in humans. Hemizygous deletions cause Williams–Beuren of protein interaction also indicates key features regarding syndrome (WBS) and duplications cause WBS duplica- the evolution of the GTF2IRD1 protein. These data provide tion syndrome. These copy number variations disturb a a visual and molecular basis for GTF2IRD1 nuclear func- variety of developmental systems and neurological func- tion that will lead to an understanding of its role in brain, tions. Human mapping data and analyses of knockout mice behaviour and human disease. show that GTF2IRD1 and GTF2I underpin the craniofacial abnormalities, mental retardation, visuospatial deficits and Abbreviations hypersociability of WBS. However, the cellular role of the hESC Human embryonic stem cells GTF2IRD1 protein is poorly understood due to its very PLA Proximity ligation assay low abundance and a paucity of reagents. Here, for the first STED Stimulated emission depletion time, we show that endogenous GTF2IRD1 has a punctate WBS Williams–Beuren syndrome pattern in the nuclei of cultured human cell lines and neu- Y2H Yeast two-hybrid rons. To probe the functional relationships of GTF2IRD1 in an unbiased manner, yeast two-hybrid libraries were screened, isolating 38 novel interaction partners, which Introduction were validated in mammalian cell lines. These relationships illustrate GTF2IRD1 function, as the isolated partners are GTF2IRD1 (GTF2I repeat domain containing protein I) was initially identified in three independent yeast one- hybrid screens as a protein that interacted with DNA baits Electronic supplementary material The online version of this composed of triplicated versions of the upstream regions article (doi:10.1007/s00439-015-1591-0) contains supplementary material, which is available to authorized users. of TNNI1 (O’Mahoney et al. 1998), Hoxc8 (Bayarsaihan and Ruddle 2000), and goosecoid (Ring et al. 2002). In the * Stephen J. Palmer human, the gene encoding GTF2IRD1 is located in a clus- [email protected] ter within chromosome 7q11.23 with two closely related 1 Cellular and Genetic Medicine Unit, School of Medical genes; GTF2I encoding TFII-I and GTF2IRD2 encoding Sciences, UNSW Australia, Sydney, NSW 2052, Australia GTF2IRD2. The 7q11.23 region contains three blocks of 2 Queensland Brain Institute, The University of Queensland, low-copy repeats (LCRs) that cause susceptibility to non- Brisbane, QLD 4072, Australia allelic homologous recombination during meiosis that 3 Centre for Neural Engineering, The University of Melbourne, results in offspring carrying hemizygous deletions result- Melbourne, VIC 3010, Australia ing in Williams–Beuren syndrome (WBS OMIM#194050) 4 Biomedical Imaging Facility, Mark Wainwright Analytical (Franke et al. 1999; Osborne et al. 1999; Pérez Jurado Centre, UNSW Australia, Sydney, NSW 2052, Australia et al. 1998; Tassabehji et al. 1999; Tipney et al. 2004) 1 3 Hum Genet or duplications that cause WBS duplication syndrome Much of the thinking regarding GTF2IRD1 func- (OMIM#609757) (Depienne et al. 2007; Merla et al. 2010; tion is based on homology with TFII-I, which has been Sanders et al. 2011; Somerville et al. 2005; Torniero et al. studied more intensively. It is undisputed that GTF2I and 2007; Van der Aa et al. 2009). GTF2IRD1 evolved from a common ancestor but the level Patients with WBS duplication syndrome have only of functional overlap and redundancy between TFII-I and recently been described and little mapping data exists GTF2IRD1 is currently unclear. Direct protein interaction that can discriminate the individual genetic contribu- between them is possible (Palmer et al. 2012) and some of tion to the phenotypes but in WBS, a series of atypical the data indicates similar target gene sets and mechanisms deletion patients indicate that loss of GTF2IRD1 and/or of regulation (Jackson et al. 2005; Palmer et al. 2012; Tan- GTF2I is necessary to manifest the craniofacial abnormal- tin et al. 2004). However, unlike GTF2IRD1, much of the ities, mental retardation, visuospatial construction defi- data on TFII-I indicate a very broad role in both the cyto- cits and hypersociability of WBS (Antonell et al. 2010). plasm and the nucleus and individual isoforms show differ- Given the profound importance of copy number variations ent subcellular localization patterns and functional proper- (CNVs) of these genes to the neurological abnormali- ties (Roy 2012). Some isoforms of TFII-I are thought to ties of WBS, it is not unreasonable to suppose that CNVs reside in the cytoplasm, where they are tethered by inter- which increase GTF2IRD1 and GTF2I gene dosage may actions with Bruton’s tyrosine kinase (Yang and Desiderio also play an important role in the consistent speech delay 1997) or p190RhoGAP (Jiang et al. 2005) and shuttle into and increased rates of autism and schizophrenia found the nucleus in response to signalling events and can also in WBS duplication syndrome and evidence from mouse interact with PLC-γ in a way that competitively inhibits its models supports this idea (Osborne 2010). Therefore, it is binding to TRPC3, thus altering agonist-induced calcium very important to understand the function of these related entry into the cell (Caraveo et al. 2006). At the same time, proteins to comprehend the consequences of their altered TFII-I isoforms have a series of nuclear roles that include dosage. direct DNA binding to the regulatory regions of various Cultured cell transfection studies and transgenic genes, including c-fos (Roy 2012). / experiments both indicate that GTF2IRD1 has strong The majority of studies indicate that Gtf2ird1− − null gene repression capabilities (Issa et al. 2006; Tay et al. mice survive but have craniofacial and neurological abnor- 2003) and binding studies demonstrated that GTF2IRD1 malities (Howard et al. 2012; Schneider et al. 2012; Tassa- / has sequence-specific DNA recognition properties for behji et al. 2005; Young et al. 2008), whereas Gtf2i− − mice GGATTA-containing sequences that are conferred by a are embryonic lethal (Enkhmandakh et al. 2009). These subset of the five I-repeat domains (RDs) that it contains data, in combination with the data on the cytoplasmic (Polly et al. 2003; Thompson et al. 2007; Vullhorst and roles of TFII-I, might be taken to suggest that TFII-I plays Buonanno 2003, 2005). The GTF2IRD1 upstream region a broader and more critical cellular role than GTF2IRD1. (GUR) contains three GGATTA binding sites and EMSA However, evolutionary conservation studies indicate that studies have shown that all three are required to achieve the common ancestor of these two genes bore a stronger high-affinity GTF2IRD1 binding (Palmer et al. 2010). This sequence similarity to the current GTF2IRD1 (Gunbin and may explain why GTF2IRD1 was readily isolated from Ruvinsky 2013). Thus, during the initial period follow- the artificial triplicated bait constructs of the original yeast ing duplication, proto-GTF2I was presumably liberated one-hybrid assays. However, it is unclear what evolutionary from functional constraints, whereas the proto-GTF2IRD1 advantage was bestowed by the multiple duplication of this retained most of the ancestral gene’s role. The GTF2I/ DNA binding domain and how the RDs work in DNA bind- GTF2IRD1 duplication pre-dates the formation of carti- ing site selection of target genes. laginous fish but the GTF2I gene has been lost in the two Apart from the RDs, the human GTF2IRD1 protein bony fish infraclasses (Teleostei and Holostei), whereas contains a short leucine zipper near the N-terminus impli- GTF2IRD1 has been retained in all vertebrates since its for- cated in dimerization (Vullhorst and Buonanno 2003), a mation (Gunbin and Ruvinsky 2013). These data support nuclear localization signal (NLS) near the C-terminus, the likelihood of functional overlaps between these two two SUMOylation motifs of which one is clearly highly proteins and suggest that, at least in bony fish, GTF2IRD1 conserved and functional (Widagdo et al. 2012), a highly is sufficient to support all of the functions they provide in conserved C-terminal domain that may be important for other species. SUMOylation due to the binding of the E3 SUMO-ligase, Based on the well-established DNA binding properties PIASxβ (Widagdo et al. 2012) and a polyserine tract near of GTF2IRD1 and the clear impact on transcriptional regu- the C-terminus that is missing in all fish species but present lation when over-expressed in vitro (Polly et al. 2003; Vull- in amphibians and may, therefore, be a more recent evolu- horst and Buonanno 2003) and in vivo (Issa et al. 2006), tionary refinement. it has been assumed that GTF2IRD1 is a conventional 1 3 Hum Genet transcription factor that has a consistent set of gene tar- result was confirmed using a pool of 4 anti-GTF2IRD1 siR- gets that will be dysregulated in its absence. But, despite NAs. While no change in the band pattern from whole cell demonstrated alterations in behaviour and motor function extracts was observed when HeLa cells were treated with in Gtf2ird1 knockout mice (Howard et al. 2012; Young control siRNA, the upper band at 130 kDa was lost when et al. 2008) and electrophysiological changes in CNS neu- cells were treated with anti-GTF2IRD1 siRNA (Fig. 1a). rons (Proulx et al. 2010), evidence for such a gene set from The lower molecular weight band detected by M19 transcriptional analysis of knockout brain tissue has so could not be identified.
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